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From "Mukhopadhyay, Aveek" <mukhopadhyay...@buckeyemail.osu.edu>
Subject RE: ctakes with uimafit
Date Mon, 22 Jul 2013 21:59:57 GMT
If instead of the 3.x lucene jars I use 4.0.0 jars then it fails with the following error

Exception in thread "main" java.lang.NoSuchMethodError: org.apache.lucene.store.RAMDirectory.<init>(Lorg/apache/lucene/store/Directory;)V

probably because the 4.x lucene.store versions do not have the RAMDirectory(directory) but
it exists in the 3.x versions. I believe I have got some version wrong, any ideas?

-aveek
________________________________
From: Mukhopadhyay, Aveek [mukhopadhyay.11@buckeyemail.osu.edu]
Sent: Monday, July 22, 2013 5:36 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit


Hello Pei,

I am using the 3.0.0-incubating version of c-takes and 3.0.1 version of the resources file.
In the pom.xml file I have the lucene version of 3.0.2.

-Aveek
________________________________
From: Chen, Pei [Pei.Chen@childrens.harvard.edu]
Sent: Monday, July 22, 2013 4:42 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit

Aveek,
Which version of cTAKES are you using (assuming it’s not trunk)?  And also, which version
of the resources file?
--Pei


From: Mukhopadhyay, Aveek [mailto:mukhopadhyay.11@buckeyemail.osu.edu]
Sent: Monday, July 22, 2013 2:49 PM
To: user@ctakes.apache.org
Subject: RE: ctakes with uimafit

Hi Murali,

Yes, I was missing fsm lib. Thanks for that.
I am encountering a different problem now. It seems it is not able to load/read the lucene
indexes and throwing up the java.io.IOException: read past EOF somewhere.

Here is the error that I am getting, any thoughts on this?

Exception in thread "main" org.apache.uima.resource.ResourceInitializationException
at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:79)
at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:165)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:190)
at com.bmi.app.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:63)
Caused by: java.io.IOException: Read past EOF
at org.apache.lucene.store.RAMInputStream.switchCurrentBuffer(RAMInputStream.java:92)
at org.apache.lucene.store.RAMInputStream.readBytes(RAMInputStream.java:76)
at org.apache.lucene.store.ChecksumIndexInput.readBytes(ChecksumIndexInput.java:45)
at org.apache.lucene.store.IndexInput.readString(IndexInput.java:124)
at org.apache.lucene.index.SegmentInfo.<init>(SegmentInfo.java:173)
at org.apache.lucene.index.SegmentInfos.read(SegmentInfos.java:258)
at org.apache.lucene.index.DirectoryReader$1.doBody(DirectoryReader.java:73)
at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:677)
at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:69)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:316)
at org.apache.lucene.index.IndexReader.open(IndexReader.java:188)
at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:69)
... 30 more

________________________________
From: Murali Nagendranath [mminnah@gmail.com]
Sent: Monday, July 22, 2013 12:09 PM
To: user@ctakes.apache.org
Subject: Re: ctakes with uimafit
Hi Aveek,


Do you have the fsm lib including in your dependencies?


Ex: http://svn.apache.org/repos/asf/ctakes/trunk/pom.xml
<dependency>


                               <groupId>net.sourceforge.openai</groupId>


                               <artifactId>openaifsm</artifactId>


<version>0.0.1</version>


                       </dependency>


-- Murali
On Mon, Jul 22, 2013 at 12:01 PM, Mukhopadhyay, Aveek <mukhopadhyay.11@buckeyemail.osu.edu<mailto:mukhopadhyay.11@buckeyemail.osu.edu>>
wrote:
Hi all,

I am trying to use the ctakes Aggregate Analysis Engine with uimafit, and I am stuck at a
problem now. Any ideas on how to solve this? I am using maven dependencies for ctakes and
have the ctakes resources project in build path.

- loading feature template
- loading lexica
- loading model
Exception in thread "main" java.lang.NoClassDefFoundError: net/openai/util/fsm/State
at org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator.initialize(ContextDependentTokenizerAnnotator.java:95)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:505)
at org.uimafit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:200)
at com.bmi.app.App.main(App.java:54)
Caused by: java.lang.ClassNotFoundException: net.openai.util.fsm.State
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 22 more


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